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Publisher Correction: Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Mar;3(3):388. doi: 10.1038/s41564-018-0114-x.


Tumour-associated and non-tumour-associated microbiota: Addendum.

Flemer B, Herlihy M, O'Riordain M, Shanahan F, O'Toole PW.

Gut Microbes. 2018 Feb 8:0. doi: 10.1080/19490976.2018.1435246. [Epub ahead of print]


How to swim with sharks: a perspective on Voltaire Cousteau's primer.

Shanahan F.

QJM. 2018 Feb 5. doi: 10.1093/qjmed/hcy027. [Epub ahead of print] No abstract available.


Determinants of Reduced Genetic Capacity for Butyrate Synthesis by the Gut Microbiome in Crohn's Disease and Ulcerative Colitis.

Laserna-Mendieta EJ, Clooney AG, Carretero-Gomez JF, Moran C, Sheehan D, Nolan JA, Hill C, Gahan CGM, Joyce SA, Shanahan F, Claesson MJ.

J Crohns Colitis. 2018 Jan 24;12(2):204-216. doi: 10.1093/ecco-jcc/jjx137.


Inclusion of the mesentery in ileocolic resection for Crohn's disease is associated with reduced surgical recurrence.

Coffey JC, Kiernan MG, Sahebally SM, Jarrar A, Burke JP, Kiely PA, Shen B, Waldron D, Peirce C, Moloney M, Skelly M, Tibbitts P, Hidayat H, Faul PN, Healy V, O Leary DP, Walsh LG, Dockery P, O Connell PR, Martin S, Shanahan F, Fiocchi C, Dunne C.

J Crohns Colitis. 2018 Jan 4. doi: 10.1093/ecco-jcc/jjx187. [Epub ahead of print]


Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Jan;3(1):8-16. doi: 10.1038/s41564-017-0072-8. Epub 2017 Dec 18. Review. Erratum in: Nat Microbiol. 2018 Feb 13;:.


CORK Study in Cystic Fibrosis: Sustained Improvements in Ultra-Low-Dose Chest CT Scores After CFTR Modulation With Ivacaftor.

Ronan NJ, Einarsson GG, Twomey M, Mooney D, Mullane D, NiChroinin M, O'Callaghan G, Shanahan F, Murphy DM, O'Connor OJ, Shortt CA, Tunney MM, Eustace JA, Maher MM, Elborn JS, Plant BJ.

Chest. 2018 Feb;153(2):395-403. doi: 10.1016/j.chest.2017.10.005. Epub 2017 Oct 14.


The oral microbiota in colorectal cancer is distinctive and predictive.

Flemer B, Warren RD, Barrett MP, Cisek K, Das A, Jeffery IB, Hurley E, O'Riordain M, Shanahan F, O'Toole PW.

Gut. 2017 Oct 7. pii: gutjnl-2017-314814. doi: 10.1136/gutjnl-2017-314814. [Epub ahead of print]


Microbial regulation of microRNA expression in the amygdala and prefrontal cortex.

Hoban AE, Stilling RM, M Moloney G, Moloney RD, Shanahan F, Dinan TG, Cryan JF, Clarke G.

Microbiome. 2017 Aug 25;5(1):102. doi: 10.1186/s40168-017-0321-3.


Editorial: probiotics in inflammatory bowel disease-wrong organisms, wrong disease, or flawed concepts?

Shanahan F.

Aliment Pharmacol Ther. 2017 Sep;46(6):632-633. doi: 10.1111/apt.14230. No abstract available.


Project DRIVE: A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening.

McDonald ER 3rd, de Weck A, Schlabach MR, Billy E, Mavrakis KJ, Hoffman GR, Belur D, Castelletti D, Frias E, Gampa K, Golji J, Kao I, Li L, Megel P, Perkins TA, Ramadan N, Ruddy DA, Silver SJ, Sovath S, Stump M, Weber O, Widmer R, Yu J, Yu K, Yue Y, Abramowski D, Ackley E, Barrett R, Berger J, Bernard JL, Billig R, Brachmann SM, Buxton F, Caothien R, Caushi JX, Chung FS, Cortés-Cros M, deBeaumont RS, Delaunay C, Desplat A, Duong W, Dwoske DA, Eldridge RS, Farsidjani A, Feng F, Feng J, Flemming D, Forrester W, Galli GG, Gao Z, Gauter F, Gibaja V, Haas K, Hattenberger M, Hood T, Hurov KE, Jagani Z, Jenal M, Johnson JA, Jones MD, Kapoor A, Korn J, Liu J, Liu Q, Liu S, Liu Y, Loo AT, Macchi KJ, Martin T, McAllister G, Meyer A, Mollé S, Pagliarini RA, Phadke T, Repko B, Schouwey T, Shanahan F, Shen Q, Stamm C, Stephan C, Stucke VM, Tiedt R, Varadarajan M, Venkatesan K, Vitari AC, Wallroth M, Weiler J, Zhang J, Mickanin C, Myer VE, Porter JA, Lai A, Bitter H, Lees E, Keen N, Kauffmann A, Stegmeier F, Hofmann F, Schmelzle T, Sellers WR.

Cell. 2017 Jul 27;170(3):577-592.e10. doi: 10.1016/j.cell.2017.07.005.


A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis.

Fouhy F, Ronan NJ, O'Sullivan O, McCarthy Y, Walsh AM, Murphy DM, Daly M, Flanagan ET, Fleming C, McCarthy M, Shortt C, Eustace JA, Shanahan F, Rea MC, Ross RP, Stanton C, Plant BJ.

Sci Rep. 2017 Jul 27;7(1):6685. doi: 10.1038/s41598-017-06880-y.


Microbial regulation of hippocampal miRNA expression: Implications for transcription of kynurenine pathway enzymes.

Moloney GM, O'Leary OF, Salvo-Romero E, Desbonnet L, Shanahan F, Dinan TG, Clarke G, Cryan JF.

Behav Brain Res. 2017 Sep 15;334:50-54. doi: 10.1016/j.bbr.2017.07.026. Epub 2017 Jul 20.


Feeding the microbiota: transducer of nutrient signals for the host.

Shanahan F, van Sinderen D, O'Toole PW, Stanton C.

Gut. 2017 Sep;66(9):1709-1717. doi: 10.1136/gutjnl-2017-313872. Epub 2017 Jun 29. Review.


Microbiota regulates visceral pain in the mouse.

Luczynski P, Tramullas M, Viola M, Shanahan F, Clarke G, O'Mahony S, Dinan TG, Cryan JF.

Elife. 2017 Jun 20;6. pii: e25887. doi: 10.7554/eLife.25887.


The microbiome regulates amygdala-dependent fear recall.

Hoban AE, Stilling RM, Moloney G, Shanahan F, Dinan TG, Clarke G, Cryan JF.

Mol Psychiatry. 2017 May 16. doi: 10.1038/mp.2017.100. [Epub ahead of print]


The effect of exercise interventions on inflammatory biomarkers in healthy, physically inactive subjects: a systematic review.

Cronin O, Keohane DM, Molloy MG, Shanahan F.

QJM. 2017 Oct 1;110(10):629-637. doi: 10.1093/qjmed/hcx091.


Erratum to: The altered gut microbiota in adults with cystic fibrosis.

Burke DG, Fouhy F, Harrison MJ, Rea MC, Cotter PD, O'Sullivan O, Stanton C, Hill C, Shanahan F, Plant BJ, Ross RP.

BMC Microbiol. 2017 Apr 27;17(1):102. doi: 10.1186/s12866-017-1006-6. No abstract available.


The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level.

Barton W, Penney NC, Cronin O, Garcia-Perez I, Molloy MG, Holmes E, Shanahan F, Cotter PD, O'Sullivan O.

Gut. 2018 Apr;67(4):625-633. doi: 10.1136/gutjnl-2016-313627. Epub 2017 Mar 30.


GREB1 genetic variants are associated with bone mineral density in Caucasians.

Hegarty KG, Drummond FJ, Daly M, Shanahan F, Molloy MG.

J Bone Miner Metab. 2018 Mar;36(2):189-199. doi: 10.1007/s00774-017-0823-x. Epub 2017 Mar 14.


Microbiome and metabolome modifying effects of several cardiovascular disease interventions in apo-E-/- mice.

Ryan PM, London LE, Bjorndahl TC, Mandal R, Murphy K, Fitzgerald GF, Shanahan F, Ross RP, Wishart DS, Caplice NM, Stanton C.

Microbiome. 2017 Mar 13;5(1):30. doi: 10.1186/s40168-017-0246-x.


The altered gut microbiota in adults with cystic fibrosis.

Burke DG, Fouhy F, Harrison MJ, Rea MC, Cotter PD, O'Sullivan O, Stanton C, Hill C, Shanahan F, Plant BJ, Ross RP.

BMC Microbiol. 2017 Mar 9;17(1):58. doi: 10.1186/s12866-017-0968-8. Erratum in: BMC Microbiol. 2017 Apr 27;17 (1):102.


Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat.

Patterson E, Wall R, Lisai S, Ross RP, Dinan TG, Cryan JF, Fitzgerald GF, Banni S, Quigley EM, Shanahan F, Stanton C.

Sci Rep. 2017 Mar 7;7:43300. doi: 10.1038/srep43300.


The influence of rosuvastatin on the gastrointestinal microbiota and host gene expression profiles.

Nolan JA, Skuse P, Govindarajan K, Patterson E, Konstantinidou N, Casey PG, MacSharry J, Shanahan F, Stanton C, Hill C, Cotter PD, Joyce SA, Gahan CGM.

Am J Physiol Gastrointest Liver Physiol. 2017 May 1;312(5):G488-G497. doi: 10.1152/ajpgi.00149.2016. Epub 2017 Feb 16.


The Gut Microbiota in Inflammatory Bowel Disease.

Sheehan D, Shanahan F.

Gastroenterol Clin North Am. 2017 Mar;46(1):143-154. doi: 10.1016/j.gtc.2016.09.011. Epub 2017 Jan 4. Review.


Gut microbiota: implications for sports and exercise medicine.

Cronin O, O'Sullivan O, Barton W, Cotter PD, Molloy MG, Shanahan F.

Br J Sports Med. 2017 May;51(9):700-701. doi: 10.1136/bjsports-2016-097225. Epub 2017 Jan 11. No abstract available.


The Changing Phenotype of Inflammatory Bowel Disease.

Moran C, Sheehan D, Shanahan F.

Gastroenterol Res Pract. 2016;2016:1619053. doi: 10.1155/2016/1619053. Epub 2016 Dec 6. Review.


Clostridium difficile carriage in adult cystic fibrosis (CF); implications for patients with CF and the potential for transmission of nosocomial infection.

Burke DG, Harrison MJ, Fleming C, McCarthy M, Shortt C, Sulaiman I, Murphy DM, Eustace JA, Shanahan F, Hill C, Stanton C, Rea MC, Ross RP, Plant BJ.

J Cyst Fibros. 2017 Mar;16(2):291-298. doi: 10.1016/j.jcf.2016.09.008. Epub 2016 Nov 29.


Unconjugated Bile Acids Influence Expression of Circadian Genes: A Potential Mechanism for Microbe-Host Crosstalk.

Govindarajan K, MacSharry J, Casey PG, Shanahan F, Joyce SA, Gahan CG.

PLoS One. 2016 Dec 1;11(12):e0167319. doi: 10.1371/journal.pone.0167319. eCollection 2016.


Adult microbiota-deficient mice have distinct dendritic morphological changes: differential effects in the amygdala and hippocampus.

Luczynski P, Whelan SO, O'Sullivan C, Clarke G, Shanahan F, Dinan TG, Cryan JF.

Eur J Neurosci. 2016 Nov;44(9):2654-2666. doi: 10.1111/ejn.13291. Epub 2016 Jul 8.


A randomised, double-blind, placebo-controlled clinical study: the effects of a synbiotic, Lepicol, in adults with chronic, functional constipation.

Cudmore S, Doolan A, Lacey S, Shanahan F.

Int J Food Sci Nutr. 2017 May;68(3):366-377. doi: 10.1080/09637486.2016.1244661. Epub 2016 Oct 24.


Quantitative analysis of mucosal oxygenation using ex vivo imaging of healthy and inflamed mammalian colon tissue.

Zhdanov AV, Okkelman IA, Golubeva AV, Doerr B, Hyland NP, Melgar S, Shanahan F, Cryan JF, Papkovsky DB.

Cell Mol Life Sci. 2017 Jan;74(1):141-151. doi: 10.1007/s00018-016-2323-x. Epub 2016 Aug 10.


Preparation of a standardised faecal slurry for ex-vivo microbiota studies which reduces inter-individual donor bias.

O'Donnell MM, Rea MC, O'Sullivan Ó, Flynn C, Jones B, McQuaid A, Shanahan F, Ross RP.

J Microbiol Methods. 2016 Oct;129:109-116. doi: 10.1016/j.mimet.2016.08.002. Epub 2016 Aug 4.


Time to abandon the hygiene hypothesis: new perspectives on allergic disease, the human microbiome, infectious disease prevention and the role of targeted hygiene.

Bloomfield SF, Rook GA, Scott EA, Shanahan F, Stanwell-Smith R, Turner P.

Perspect Public Health. 2016 Jul;136(4):213-24. doi: 10.1177/1757913916650225.


Microbial contributions to chronic inflammation and metabolic disease.

Shanahan F, Sheehan D.

Curr Opin Clin Nutr Metab Care. 2016 Jul;19(4):257-62. doi: 10.1097/MCO.0000000000000282. Review.


Regulation of prefrontal cortex myelination by the microbiota.

Hoban AE, Stilling RM, Ryan FJ, Shanahan F, Dinan TG, Claesson MJ, Clarke G, Cryan JF.

Transl Psychiatry. 2016 Apr 5;6:e774. doi: 10.1038/tp.2016.42.


Tumour-associated and non-tumour-associated microbiota in colorectal cancer.

Flemer B, Lynch DB, Brown JM, Jeffery IB, Ryan FJ, Claesson MJ, O'Riordain M, Shanahan F, O'Toole PW.

Gut. 2017 Apr;66(4):633-643. doi: 10.1136/gutjnl-2015-309595. Epub 2016 Mar 18.


Exercise, fitness, and the gut.

Cronin O, Molloy MG, Shanahan F.

Curr Opin Gastroenterol. 2016 Mar;32(2):67-73. doi: 10.1097/MOG.0000000000000240. Review.


IL-36α expression is elevated in ulcerative colitis and promotes colonic inflammation.

Russell SE, Horan RM, Stefanska AM, Carey A, Leon G, Aguilera M, Statovci D, Moran T, Fallon PG, Shanahan F, Brint EK, Melgar S, Hussey S, Walsh PT.

Mucosal Immunol. 2016 Sep;9(5):1193-204. doi: 10.1038/mi.2015.134. Epub 2016 Jan 27.


Pure Iterative Reconstruction Improves Image Quality in Computed Tomography of the Abdomen and Pelvis Acquired at Substantially Reduced Radiation Doses in Patients With Active Crohn Disease.

McLaughlin PD, Murphy KP, Twomey M, OʼNeill SB, Moloney F, OʼConnor OJ, OʼRegan K, McSweeney S, McGarrigle AM, Moore N, Bye J, Shanahan F, Maher MM.

J Comput Assist Tomogr. 2016 Mar-Apr;40(2):225-33. doi: 10.1097/RCT.0000000000000358.


How mothers mediate the social integration of their children conceived of forced marriage within the Lord's Resistance Army.

Shanahan F, Veale A.

Child Abuse Negl. 2016 Jan;51:72-86. doi: 10.1016/j.chiabu.2015.11.003. Epub 2015 Dec 6.


Model-Based Iterative Reconstruction in CT Enterography.

Murphy KP, Crush L, Twomey M, McLaughlin PD, Mildenberger IC, Moore N, Bye J, O'Connor OJ, McSweeney SE, Shanahan F, Maher MM.

AJR Am J Roentgenol. 2015 Dec;205(6):1173-81. doi: 10.2214/AJR.14.13321.


Differential expression of key regulators of Toll-like receptors in ulcerative colitis and Crohn's disease: a role for Tollip and peroxisome proliferator-activated receptor gamma?

Fernandes P, MacSharry J, Darby T, Fanning A, Shanahan F, Houston A, Brint E.

Clin Exp Immunol. 2016 Mar;183(3):358-68. doi: 10.1111/cei.12732. Epub 2015 Nov 26.


Microbes & neurodevelopment--Absence of microbiota during early life increases activity-related transcriptional pathways in the amygdala.

Stilling RM, Ryan FJ, Hoban AE, Shanahan F, Clarke G, Claesson MJ, Dinan TG, Cryan JF.

Brain Behav Immun. 2015 Nov;50:209-220. doi: 10.1016/j.bbi.2015.07.009. Epub 2015 Jul 14.


Prognostic significance of prospectively detected bone marrow micrometastases in esophagogastric cancer: 10-year follow-up confirms prognostic significance.

Ryan P, Furlong H, Murphy CG, O'Sullivan F, Walsh TN, Shanahan F, O'Sullivan GC.

Cancer Med. 2015 Aug;4(8):1281-8. doi: 10.1002/cam4.470. Epub 2015 Apr 27.


The microbiota in inflammatory bowel disease.

Sheehan D, Moran C, Shanahan F.

J Gastroenterol. 2015 May;50(5):495-507. doi: 10.1007/s00535-015-1064-1. Epub 2015 Mar 26. Review.


Exercise and the microbiota.

O'Sullivan O, Cronin O, Clarke SF, Murphy EF, Molloy MG, Shanahan F, Cotter PD.

Gut Microbes. 2015;6(2):131-6. doi: 10.1080/19490976.2015.1011875. Epub 2015 Mar 24.


In the performing art of medicine: the doctor as actor.

Whorwell PJ, Shanahan F.

QJM. 2016 Mar;109(3):159-60. doi: 10.1093/qjmed/hcv053. Epub 2015 Feb 24. No abstract available.


Separating the microbiome from the hyperbolome.

Shanahan F.

Genome Med. 2015 Feb 24;7(1):17. doi: 10.1186/s13073-015-0143-5. eCollection 2015.


Adult Hippocampal Neurogenesis Is Regulated by the Microbiome.

Ogbonnaya ES, Clarke G, Shanahan F, Dinan TG, Cryan JF, O'Leary OF.

Biol Psychiatry. 2015 Aug 15;78(4):e7-9. doi: 10.1016/j.biopsych.2014.12.023. Epub 2015 Jan 9. No abstract available.


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